Enterococcus species are members of the normal flora of the gastrointestinal tract in humans and animals and have emerged as a leading cause of nosocomial infection. The two major pathogenic species in humans are Enterococcus faecalis (E. faecalis) and E. faecium, with occasional infections being caused by E. durans, E. gallinarum, E. casseliflavus, E. avium, E. hirae, E. mundtii, and E. raffinosus. Enterococcal infections are particularly troublesome because of the high level of intrinsic antibiotic resistance.
Enterococci are routinely used as indicator organisms to assess the quality of recreational waters. Elevated concentrations of enterococci, particularly E. faecalis, E. faecium and E. durans, are indicative of fecal contamination and the presence of enteric pathogens. Rapid detection of enterococci in the environment is of importance in reducing the spread of multiresistant enterococci and also in assessing the quality of recreational waters.
Conventional methods for Enterococcus detection based on cultivation often require 1 to 2 days. Such methods are further hampered by growing bacteria in artificial media that contributes to the poor culturability of injured and stressed organisms as well as the ability of enterococci to enter a viable but nonculturable state.
The methods and compositions described herein, based on the detection of specific rRNA sequences unique to Enterococcus species indicative of fecal contamination (hereinafter “indicator enterococci”), allow rapid, sensitive, and specific detection of E. faecalis, E. faecium, E. casseliflavus, E. gallinarum, E. mundtii, E. durans, E. hirae, and E. columbae without detection of E. avium, E. malodoratus, E. pseudoavium, E. raffinosus, E. saccharolyticus, and E. dispar. 